In general, a mass spectrometer comprises an ion source for generating ions from molecules to be analysed, and ion optics for guiding the ions to a mass analyser. A tandem mass spectrometer further comprises a second mass analyser. In tandem mass spectrometry, structural elucidation of ionised molecules is performed by collecting a mass spectrum, then using a first mass analyser to select a desired precursor ion or ions from the mass spectrum, causing fragmentation of ions, and then performing mass analysis of the fragment ions using a second mass analyser. Generally, a mass analyser with accurate mass capability is preferable for the second mass analyser. It is often desirable to obtain a mass spectrum of precursor ions also using the accurate mass analyser, i.e. pass a sample of precursor ions to the accurate mass analyser without fragmentation.
The method can be extended to provide one or more further stages of fragmentation (i.e. fragmentation of fragment ions and so on). This is typically referred to as MSn, with n denoting the number of generations of ions. Thus MS2 corresponds to tandem mass spectrometry.
Tandem mass spectrometers can be classified into three types:
(1) sequential in space, corresponding to combinations of transmitting mass analysers (e.g. magnetic sectors, quadrupole, time-of-flight (TOF), usually with a collision cell in-between);
(2) sequential in time, corresponding to stand-alone trapping mass analysers (e.g. quadrupole, linear, Fourier transform ion cyclotron resonance (FT-ICR), electrostatic traps); and
(3) sequential in time and space, corresponding to hybrids of traps or hybrids of traps and transmitting mass analysers.
This invention is particularly well suited for use with pulsed accurate-mass analysers, such as TOF analysers, FT ICR analysers and electrostatic trap (EST) analysers such as the Orbitrap mass analyser.
Most of these analysers have a short injection cycle followed by relatively long mass analysis stage, especially when operated at high resolution. Therefore, their sensitivity greatly benefits from using an intermediate ion store such as a RF multipole.
Frequently, accurate-mass analysers are preceded by stages of mass analysis, for example tandem mass spectrometry as described above. These first stages of mass spectrometry may include ion trapping in a quadrupole trap or any other known mass analyser. In these instances, use of an intermediate ion store avoids ion losses caused by differences in repetition rates and ion beam parameters between the different stages. Examples of tandem mass spectrometers including an intermediate ion store may be found in J. Proteome Res. 3(3) (2004) pp 621-626, Anal Chem. 73 (2001) p 253, WO2004/068523, US 2002/0121594, US2002/0030159, WO99/30350 and WO02/078046. Other tandem configurations are also possible.
Ion traps used as mass analysers are always sensitive to the total number of ions introduced and trapped therein. Clearly, it is desirable to accumulate as many ions as possible in the mass analyser in order to improve the statistics of the collected data. However, this desideratum is in conflict with the fact that there is saturation at higher ion concentrations that produces space charge effects. These space charge effects limit mass resolution and cause shifts of measured mass-to-charge ratios, thereby leading to incorrect assignment of masses and even intensities. In particular, overfilling the intermediate ion store with ions causes peak shifts in the subsequently obtained mass spectra, loss of mass accuracy in a trapping mass analyser, and saturation of the detector in a TOF mass analyser, besides mass suppression effects in the intermediate ion store itself.
One technique that addresses this problem is generally referred to as automatic gain control (AGC). AGC is the common name for utilisation of information about an incoming ion stream to regulate the amount of ions admitted to a mass analyser. This information may also be used to select mass ranges, based on spectral information. The total ion abundance accumulated within an ion trap may be controlled as follows. First, ions are accumulated over a known time period and a rapid total ion abundance measurement is performed. Knowledge of the time period and the total ion abundance in the trap allows selection of an appropriate filling time for subsequent ion fills to create an optimum ion abundance in the cell. This technique is described in further detail in U.S. Pat. No. 5,107,109.
Different variants of measuring the initial ion abundance are known, including using the total ion current in the previous spectra (U.S. Pat. No. 5,559,325); using a short pre-scan in which ions are transmitted through the trap towards the detector (WO03/019614); and measuring a part of the ions stored in storage multipole prior to FT ICR (U.S. Pat. No. 6,555,814).
In the majority of tandem mass spectrometers with accurate mass analysers, the ion population accumulated is not controlled at all. In the case of J. Proteome Res. 3(3) (2004) pp 621-626, only the total ion number prior to injection into the accurate-mass analyser could be controlled using automatic gain control. WO2004/068523 discloses an embodiment that includes an intermediate ion store used to accumulate multiple fills of an ion type from a linear trap prior to injecting all of the ions into a FT ICR mass analyser. Each fill has its own automatic gain control pre-scan prior to injecting ions into an intermediate ion store. However, its primary application is only the increase of total ion storage capacity relative to operating a single ion trap.
This leaves unattended some real-life problems. Often it is desirable to analyze more than a single type of ion, i.e. ions having a single m/z value or a m/z range. The different types of ions may be derived from different requirements according to any particular experiment. For example, the different types of ions may originate from different molecules present in a sample, from sample ions that are fragmented in tandem mass spectrometry (i.e. analysis of precursor and fragment ions), or from sample ions and calibrant ions (i.e. lock masses used for correction of mass spectra). The last case is very important as the use of internal calibrants is known to be one of the most reliable ways of improving mass accuracy (especially for TOF and EST), using analytes added or inherently present in the incoming sample. However, it is very difficult to obtain a desired abundance of internal calibrant when the analyte signal is changing rapidly, for example as with liquid separations coupled to the mass spectrometer. This poses a significant problem because accuracy of the calibrant abundance is very important: if the abundance is too low, the calibrant is useless for improving mass accuracy; if the abundance is too high, the calibrant ions occupy most of the space charge capacity of the intermediate ion store and so reduce sample utilisation. It is also very difficult to enrich ion population selectively with components of choice (e.g. impurities of interest).
With the aim of internal calibration of mass spectra, two methods of combining ions from two or more ion sources have been developed: Winger et al. (Proc. 44th Conf. Amer. Soc. Mass Spectrom., Portland, 1996, p. 1134) demonstrated simultaneous trapping of ions from two sources introduced into an ICR cell from two directions, as well as the combination of ions generated by electron ionisation in an ICR cell with externally injected ions. U.S. Pat. No. 5,825,026 demonstrates a mechanically switchable structure that allows ions from two ion sources to be selected for introduction into a mass analyser.